The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses*

Abstract

Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility of proteomic laboratories over an extended period of time. Developed as an open study, initially 64 participants were recruited from the broader mass spectrometry community to analyze provided aliquots of a six bovine protein tryptic digest mixture every month for a period of nine months. Data were uploaded to a central repository, and the operators answered an accompanying survey. Ultimately, 45 laboratories submitted a minimum of eight LC-MSMS raw data files collected in data-dependent acquisition (DDA) mode. No standard operating procedures were enforced; rather the participants were encouraged to analyze the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration, but rather to assess the temporal intralaboratory reproducibility. The outcome of the study was reassuring with 80% of the participating laboratories performing analyses at a medium to high level of reproducibility and quality over the 9-month period. For the groups that had one or more outlying experiments, the major contributing factor that correlated to the survey data was the performance of preventative maintenance prior to the LC-MSMS analyses. Thus, the Protein Research Group of the Association of Biomolecular Resource Facilities recommends that laboratories closely scrutinize the quality control data following such events. Additionally, improved quality control recording is imperative. This longitudinal study provides evidence that mass spectrometry-based proteomics is reproducible. When quality control measures are strictly adhered to, such reproducibility is comparable among many disparate groups. Data from the study are available via ProteomeXchange under the accession code PXD002114. Molecular & Cellular Proteomics 14: 10.1074/mcp.O115.051888, 3299-3309, 2015.The broad-reaching use and application of mass spectrometry-based proteomics in the international research commu-

Variations of Histone Modification Patterns: Contributions of Inter-plant Variability and Technical Factors

“…Results of an LMM including data for the affected batch (presented in Supplementary Figure 3 ) show that factors such as an essential service intervention between runs may significantly reduce reproducibility, and analysis of an additional technical batch is warranted in such cases. Other factors that may contribute to a reduction in technical reproducibility have been identified in a recent intra-laboratory variability survey by the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) ( Bennett et al, 2015 ). Interestingly, a substantial association between preventative maintenance of the instrument prior to LC-MS/MS analyses and frequencies of outliers was reported, so the ABRF-PRG emphasized the need for thorough quality control after such events.…”

Quality control in mass spectrometry‐based proteomics

“…As represented in Figure , this variability can originate from multiple sources: the different stages of an LC‐MS experiment can each exhibit stochastic behavior and influence one another, contaminants can inadvertently be present and the optimal computational interpretation is often not obvious . Furthermore, instrument drift and sample degradation can introduce a longitudinal variability . Most notably, instrument interventions, such as a preventive maintenance, have a considerable influence upon the results .…”

“…Furthermore, instrument drift and sample degradation can introduce a longitudinal variability . Most notably, instrument interventions, such as a preventive maintenance, have a considerable influence upon the results . Especially in regard to current large‐scale studies this is of major importance, as measurements obtained at different times can only be correctly compared with each other if they were obtained under consistent and comparable conditions.…”

“…24,25 Most notably, instrument interventions, such as a preventive maintenance, have a considerable influence upon the results. 24 Especially in regard to current large-scale studies this is of major importance, as measurements obtained at different times can only be correctly compared with each other if they were obtained under consistent and comparable conditions. Therefore, in order to inspire confidence in the obtained results, it is of vital importance that appropriate quality assurance (QA) and quality control (QC) measures are taken to monitor and control the existing variability.…”

MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments

“…Likewise, bean plots and run charts were used to monitor QC metrics with Metriculator (27), however, the tool did not implement thresholds for distinguishing undesirable system variation from noise. Bennett et al (28) analyzed multisite DDA experiments with QuaMeter and NISTMSQC. The authors used principle component analysis and control charts to highlight patterns of between-laboratory variation, however the longitudinal aspect of the study was limited to only nine time points.…”